<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
<html>
<head>
<meta http-equiv="Content-Type" content="text/html;charset=iso-8859-1">
<title>MRtrix documentation</title>
<link rel="stylesheet" href="../stylesheet.css" type="text/css" media=screen>
</head>
<body>

<table class=nav>
<tr>
<td><a href="../faq.html"><img src="../left.png"></a></td>
<td><a href="../index.html"><img src="../up.png"></a></td>
<td><a href="../index.html"><img src="../home.png"></a></td>
<th>list of MRtrix commands</th>
<td><a href="../appendix/index.html"><img src="../right.png"></a></td>
</tr>
</table>
<table class=cmdindex width=100%>
<tr><td><a href="average.html">average</a></td><td>average an image along a specific axis.</td></tr>
<tr><td><a href="bogus.html">bogus</a></td><td>this is used to test stuff.</td></tr>
<tr><td><a href="csdeconv.html">csdeconv</a></td><td>perform non-negativity constrained spherical deconvolution.</td></tr>
<tr><td><a href="dicom_filename.html">dicom_filename</a></td><td>read a DICOM file and output a suitable filename for its storage.</td></tr>
<tr><td><a href="dir2amp.html">dir2amp</a></td><td>convert directions image to amplitudes.</td></tr>
<tr><td><a href="disp_profile.html">disp_profile</a></td><td>view spherical harmonics surface plots.</td></tr>
<tr><td><a href="dwi2SH.html">dwi2SH</a></td><td>convert base diffusion-weighted images to their spherical harmonic representation.</td></tr>
<tr><td><a href="dwi2tensor.html">dwi2tensor</a></td><td>convert diffusion-weighted images to tensor images.</td></tr>
<tr><td><a href="erode.html">erode</a></td><td>erode (or dilate) mask (i.e. binary) image</td></tr>
<tr><td><a href="estimate_response.html">estimate_response</a></td><td>estimate the fibre response function for use in spherical deconvolution.</td></tr>
<tr><td><a href="find_SH_peaks.html">find_SH_peaks</a></td><td>identify the orientations of the N largest peaks of a SH profile</td></tr>
<tr><td><a href="gen_WM_mask.html">gen_WM_mask</a></td><td>generate a white matter probability mask from the DW images.</td></tr>
<tr><td><a href="gendir.html">gendir</a></td><td>generate a set of directions evenly distributed over a hemisphere.</td></tr>
<tr><td><a href="import_tracks.html">import_tracks</a></td><td>convert ascii track files into MRtrix format.</td></tr>
<tr><td><a href="median3D.html">median3D</a></td><td>smooth images using a 3x3x3 median filter.</td></tr>
<tr><td><a href="mradd.html">mradd</a></td><td>add or subtract images</td></tr>
<tr><td><a href="mrcat.html">mrcat</a></td><td>concatenate several images into one</td></tr>
<tr><td><a href="mrconvert.html">mrconvert</a></td><td>perform conversion between different file types and optionally extract a subset of the input image.</td></tr>
<tr><td><a href="mrinfo.html">mrinfo</a></td><td>display header information</td></tr>
<tr><td><a href="mrmult.html">mrmult</a></td><td>multiply images</td></tr>
<tr><td><a href="mrstats.html">mrstats</a></td><td>compute images statistics.</td></tr>
<tr><td><a href="mrtransform.html">mrtransform</a></td><td>apply spatial transformations or reslice images.</td></tr>
<tr><td><a href="mrview.html">mrview</a></td><td>the MRtrix image viewer.</td></tr>
<tr><td><a href="normalise_tracks.html">normalise_tracks</a></td><td>apply a normalisation map to a tracks file.</td></tr>
<tr><td><a href="read_dicom.html">read_dicom</a></td><td>output DICOM fields in human-readable format.</td></tr>
<tr><td><a href="read_ximg.html">read_ximg</a></td><td>output XIMG fields in human-readable format.</td></tr>
<tr><td><a href="sdeconv.html">sdeconv</a></td><td>perform linear spherical deconvolution.</td></tr>
<tr><td><a href="streamtrack.html">streamtrack</a></td><td>perform streamlines tracking.</td></tr>
<tr><td><a href="tensor2ADC.html">tensor2ADC</a></td><td>calculate map of mean apparent diffusion coefficient (ADC) from diffusion tensor image.</td></tr>
<tr><td><a href="tensor2FA.html">tensor2FA</a></td><td>calculate map of fractional anisotropy from diffusion tensor image.</td></tr>
<tr><td><a href="tensor2vector.html">tensor2vector</a></td><td>generate map of the major eigenvector.</td></tr>
<tr><td><a href="tensor_metric.html">tensor_metric</a></td><td>generate maps of tensor-derived parameters.</td></tr>
<tr><td><a href="threshold.html">threshold</a></td><td>create bitwise image by thresholding image intensity.</td></tr>
<tr><td><a href="track_info.html">track_info</a></td><td>print out information about track file</td></tr>
<tr><td><a href="tracks2prob.html">tracks2prob</a></td><td>convert a tracks file into a map of the fraction of tracks to enter each voxel.</td></tr>
</table>
</body>
</html>